The "coverage" tool is a great addition to the set, but I think the description is backwards from the execution.
The user selects:
The density of elements of Query: (call it query 1)
within Query: (call it query 2)
The explanation says:
"Return entire regions from query 1 that overlap query2, and append two more fields at the end of the returned region: (1) the number of nucleotides for each returned region from query 1 that overlap a region from query 2 and (2) the percentage of the overlap for each region of query1: ..."
What you get is actually the opposite of the explanation. You get the regions from the 2nd query that contain regions from query 1, etc. The selection tools have query 2 as the target for finding elements from query 1, but the explanation treats query 1 as the target.
I think the first choice should be query 1 and the second choice be query 2. You could change the explanation, but I think it would be better to change the selection display. In that case, you would have something like:
Within Query: (pull down menu of choices for the target)
Find the density of elements of Query: (pull down menu of choices for elements to find in the target).
Then the explanation will fit.
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
phone: 814-863-0113 FAX: 814-863-7024